Table 1.

The key driver elements identified TF-gene interactions and miRNA-mRNA interactions.

	Module	Gene count	Top GO category	Top KEGG categories	Key driver count	Key drivers
TF-mRNA interactions	black	41	Regulation of transcription	Pathways in cancer, Renal cell carcinoma	5	SORBS3, ZNF43, ZNF681, RBMX, POU2F1
	blue	247	Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	Cell cycle, Prostate cancer, Melanoma	9	AR, BRCA1, ESR1, JUN, MYB, RPN1, E2F1, E2F2, PPARD
	brown	195	Anatomical structure morphogenesis	Leukocyte transendothelial migration	5	TMOD3, CREB1, POU5F1, SP3, TERT
	green	110	Cellular macromolecule metabolic process	Endometrial cancer, Insulin signaling pathway	15	B4GALT7, OS9, CDC34, MAN2C1, MYO1C, SH3GLB2, INPP5E, PLXNB1, USF2, PPP1R12C, CDK9, DAP, E4F1, E2F4, USF1
	grey	148	Anatomical structure development	Sulfur metabolism	18	AHCTF1, NQO2, FGFR2, CCDC130, ABCG4, BIRC6, CA6, SP4, RNF2, SPRR1B, C16orf65, DNAJC5G, SNCAIP, GRIK5, SLC6A4, SMAD1, DAD1, POU4F2
	magenta	26	Regulation of metabolic process	p53 signaling pathway, Alzheimer's disease	3	ATF6, NGEF, POGK
	pink	30	Transcription initiation from RNA polymerase II promoter	Basal transcription factors	4	CCDC92, TMEM70, RNF139, E2F5
	red	93	Regulation of cellular process	Endometrial cancer, Neurotrophin signaling pathway	14	ATP1B1, STAT3, ABCB8, MYC, TGFB1, SP1, TP53, PCGF1, SUMF2, GTF3A, IPO13, GMPPA, HTR6, TGIF1
	turquoise	295	Regulation of cellular metabolic process	p53 signaling pathway, Pancreatic cancer, Apoptosis	2	UBL5, RNF111
	yellow	132	Immune system process	Chemokine signaling pathway, Natural killer cell mediated cytotoxicity	19	APOC1, CD2, CD79B, LRRC28, DAPK1, FAM124B, EML2, LAP3, TSPAN2, FCRL3, ELMO1, SLC7A7, RASSF5, SLC31A2, TRAF3IP3, GALNT12, ITGA4, SPI1, TFAP2A
	Total	1317
miRNA-mRNA interactions	Genes	Gene count	Top GO category	Top KEGG categories	Key driver count	Key drivers
		869	Regulation of macromolecule metabolic process	Pathways in cancer, Pancreatic cancer, Prostate cancer	17	MYC, ATG4C, TGFB1, NFKB1, AKT1, EGR1, TP53, SOX10, SPI1, MECP2, E2F3, CREB1, TCF3, TPP1, FLICE, LPS, PACS1
	miRNAs	miRNA count	Top functional categories	Top HMDD categories	Key driver count	Key drivers
		120	miRNA tumor suppressors, immune response, Onco-miRNA, cell death, human embryonic stem cells regulation	Breast cancer (65), Neoplasms (58), Melanoma (56), Ovarian Neoplasms (51), Pancreatic Neoplasms (38), Prostatic Neoplasms (38)	68	mir-126, mir-609, mir-488, mir-191, mir-200c, mir-200a, mir-30a, mir-30d, mir-335, mir-190b, mir-223, mir-106b, mir-519e, mir-210, mir-379, mir-203, mir-205, mir-708, mir-29c, mir-29a, mir-182, mir-183, mir-127, mir-187, mir-425, let-7g, let-7d, mir-152, mir-155, mir-21, mir-22, mir-758, mir-921, mir-922, mir-375, mir-377, mir-181a-2, mir-657, mir-302d, mir-100, mir-10b, mir-10a, mir-625, mir-629, mir-92a-2, mir-26b, mir-25, mir-145, mir-143, mir-141, mir-221, mir-193b, mir-193a, mir-374a, mir-134, mir-146a, mir-31, let-7a-2, mir-27a, mir-27b, mir-133a-1, let-7i, mir-93, mir-23a, mir-148a, mir-196a-2, mir-487b, mir-149

For the 10 gene modules identified in TF-mRNA interactions, we list counts of the involved genes, the most significant GO and KEGG terms, and the identified key driver genes from each module. Similarly for the miRNA-mRNA interactions, we list the key driver molecules of both genes and miRNAs. The driver genes, whose protein products are known to be targeted by drugs, are in bold.